Align Serine transporter (characterized)
to candidate GFF2931 PS417_14995 serine/threonine protein kinase
Query= SwissProt::P0AAD6 (429 letters) >FitnessBrowser__WCS417:GFF2931 Length = 425 Score = 556 bits (1432), Expect = e-163 Identities = 280/414 (67%), Positives = 339/414 (81%), Gaps = 8/414 (1%) Query: 16 SAWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILAFPMTFFAHRGLTRFV 75 ++W + DT WMLGL+GTAIGAG LFLPINAG+GG PL+I+A+LAFPMTFFAHRGLTRFV Sbjct: 20 TSWSRQDTTWMLGLFGTAIGAGTLFLPINAGLGGFWPLVILALLAFPMTFFAHRGLTRFV 79 Query: 76 LSGKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAITNTVESFMSHQLGMT 135 LSG+ G DIT+VVEEHFGI AG LITLLYFFAI+PILL+YSVA+TNTV SFM HQL + Sbjct: 80 LSGRE-GSDITDVVEEHFGIKAGALITLLYFFAIFPILLIYSVALTNTVGSFMEHQLHIM 138 Query: 136 PPPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLALYLIPQWNGAALETL 195 PPPRAILS +LI+G++ +VR GEQ+IVKAMS++V+PF+ L+ LA+YLIP WNG L T Sbjct: 139 PPPRAILSFVLILGLLAVVRCGEQVIVKAMSLMVYPFIVALLFLAVYLIPHWNGGILSTA 198 Query: 196 SLDTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYGDMAEQKCSKILAFAH 255 S T + L TLWLAIPVMVFSFNHSPIIS+FAV ++ +YG A+++ S+IL+ AH Sbjct: 199 S---QVPTPSALLNTLWLAIPVMVFSFNHSPIISAFAVDQKRQYGIHADERSSQILSRAH 255 Query: 256 IMMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPVIAWMAPIIAIIAITK 315 ++MV+ V+FFVFSCVL+L+PA LA AK QN+SILSYLANHFN P I + AP+IA +AITK Sbjct: 256 LLMVVMVLFFVFSCVLTLSPAQLAEAKAQNLSILSYLANHFNNPTIEFAAPLIAFVAITK 315 Query: 316 SFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTTWIVATLNPSILGMIE 375 SFLGHY+GA EG G+V+K+ R G +L+R+TA FMLV WIVATLNPSILGMIE Sbjct: 316 SFLGHYIGASEGLKGLVLKTGRRPG----AKRLDRMTAAFMLVVCWIVATLNPSILGMIE 371 Query: 376 TLGGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAISAIFYSLFS 429 LGGPIIA ILFLMPMYAI+KVPAM KY G SNVFV +GL+AI+A+ YSLF+ Sbjct: 372 ALGGPIIASILFLMPMYAIRKVPAMAKYRGQASNVFVTAVGLVAITAVVYSLFA 425 Lambda K H 0.328 0.140 0.416 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 627 Number of extensions: 31 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 429 Length of database: 425 Length adjustment: 32 Effective length of query: 397 Effective length of database: 393 Effective search space: 156021 Effective search space used: 156021 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory